Coding variant associations format

Coding variant association analysis results for imputed data aggregated across all phenotypes.

Files:

coding_variants.tsv.gz: binary endpoints

coding_variants.quantitative.tsv.gz: quantitative phenotypes

Files are compressed tabix-indexed files containing all coding variants across all regenie-analysed phenotypes with following conditions:

1. P-value < 1e-4

2. Variant is categorized as one of the following:

• transcript_ablation

• splice_donor_variant

• stop_gained

• splice_acceptor_variant

• frameshift_variant

• stop_lost

• start_lost

• inframe_insertion

• inframe_deletion

• missense_variant

• protein_altering_variant

File columns:

Column name	Description
#chrom	Chromosome
pos	Position
ref	Reference allele
alt	Alternative allele
pval	P-value
mlogp	#NAME?
beta	Beta
sebeta	Standard error
af_alt	Alternative allele frequency
af_alt_cases	Alternative allele frequency in cases (non-quantitative only)
af_alt_controls	Alternative allele frequency in controls (non-quantitative only)
fin.AF	Alternative allele frequency in the Finnish population (GnomAD)
nfsee.AF	Alternative allele frequency in the non-Finnish-Swedish-Estonian European population (GnomAD)
rsid	rsID
gene_most_severe	Nearest gene
most_severe	Variant type
fin.enrichment	Finnish enrichment (fin.AF / nfsee.AF)
phenotype	Phenotype abbreviation